Preservation and Preservatives
Heather A.E. Benson, Michael S. Roberts, Vânia Rodrigues Leite-Silva, Kenneth A. Walters in Cosmetic Formulation, 2019
When evaluating preservatives and preservative combinations in the development stage of the process, it is common practice to determine the minimum inhibitory concentration (mic) value. This is the lowest concentration at which the test substance prevents further growth of the test organism. This value is specific to both the substance and the organism tested. The concentration required to kill the organism is usually much higher than the mic value. Manufacturers of preservatives usually offer mic data in support of their products, but this information should be treated with a little caution. There is no standard method for the mic test and the results are subject to wide variability, as there are several factors that have a significant effect on the result. The most important variables are the inoculum count employed and the actual strain of the test organism. The lower the inoculum count, the lower the concentration of test substance required to prevent cells from growing, and it is possible to manipulate the data by using a low inoculum count to produce low mic figures, thereby making the test substance appear unduly active. Microbial cells from all species evolve and adapt to their surroundings, and microbial resistance, or tolerance, can develop in laboratory strains, leading to incorrect mic results. There is also the potential for huge variability in response between the different strains of the same species. (A strain is a subset of a bacterial species differing from other bacteria of that species by some minor but identifiable difference.)
An Overview of Parasite Diversity
Eric S. Loker, Bruce V. Hofkin in Parasitology, 2015
First we introduce several terms that are applied to variant forms within a species. The term isolate describes a sample of a parasite species derived from a particular host at a particular time. Strain refers to an intraspecific group of parasites that differs from other such groups in one or more traits, including traits that might be relevant to control or treatment. Subspecies is used to identify a distinctive group of organisms within a species that may occupy a particular region and that can interbreed with other subspecies. In this case, however, the organisms typically do not interbreed because of their isolation or another reason. Subspecies are given a formal name, such as Trypanosoma brucei rhodesiense, with rhodesiense being the subspecies name. Also, whereas studies to discriminate among species rely on less variable genetic markers such as SSU rDNA or cytochrome oxidase (see Section 2.3), studies of intraspecific diversity rely on more variable markers, such as other genes or sequences associated with the mitochondrial genome, or microsatellite markers. Microsatellite markers are short repeat sequences (usually 2 to 6 nucleotides long) that undergo rapid change in the number of times they are duplicated, providing a good way to discriminate among individual parasites.
An Overview of Parasite Diversity
Eric S. Loker, Bruce V. Hofkin in Parasitology, 2023
First we introduce several terms that are applied to variant forms within a species. The term isolate describes a sample of a parasite species derived from a particular host at a particular time. Strain refers to an intraspecific group of parasites that differs from other such groups in one or more traits, including traits that might be relevant to control or treatment. Subspecies is used to identify a distinct group of organisms within a species that may occupy a particular region and that can interbreed with other subspecies. In this case, however, the organisms typically do not interbreed because of their isolation or some other reason. Subspecies are given a formal name, such as Trypanosoma brucei rhodesiense, with rhodesiense being the subspecies name. Also, although studies to discriminate among species use less variable genetic markers such as SSU rDNA or cytochrome oxidase, studies of intraspecific diversity rely on more variable markers, such as microsatellite markers or single nucleotide polymorphisms (SNPs, pronounced “snips).” See Figure 7.2 for further details. Both microsatellite markers and SNPs can be used to differentiate one individual parasite from another or to identify differences among populations of the same parasite species across small geographic scales.
Mucin degrader Akkermansia muciniphila accelerates intestinal stem cell-mediated epithelial development
Published in Gut Microbes, 2021
Seungil Kim, Yun-Chan Shin, Tae-Young Kim, Yeji Kim, Yong-Soo Lee, Su-Hyun Lee, Mi-Na Kim, Eunju O, Kwang Soon Kim, Mi-Na Kweon
Individual bacterial strains, even the same species, have strain-specific abilities. As lactic acid bacterial strains of the same species show different enzymatic activities,49 we wondered whether different A. muciniphila strains might have varying effects on ISC-mediated epithelial development. We found that the newly identified A. muciniphila AK32 strain activated the expression of genes involved in SCFA production and increased the secretion of acetic and propionic acids. As expected, promoter sequences of mmd in AK32 differed by type strain, but those of pdh were highly conserved. The detailed mechanism by which expression occurs is yet to be determined. We did identify a strain-specific alteration of the Mmd amino acid sequence, which may influence enzyme activity by altering propionic acid levels. Thus, we conclude that strain AK32 has a characteristic genome, unlike the A. muciniphila type strain, leading to increased SCFA production, especially acetic and propionic acids.
Strategic advancements and multimodal applications of biofilm therapy
Published in Expert Opinion on Biological Therapy, 2021
Infective endocarditis, a disorder showed death rates ranging from 25 to 40% and required antibiotics for the treatment where responses were obtained from the positive blood samples [113]. Furthermore, the culture-dependant microbiological diagnosis test detected the microbial species but the strain and genotype properties of bacteria were unidentified. The S. aureus species was widely responsible for infective endocarditis and identifying the bacterial strain which was clinically important. This microbe leads to severe inflammations and toxicity dependant on the various virulence factors present in S. aureus strains [114]. Efficient properties of S. aureus and detection of viral factors were obtained by cell culture-based assays (CCBA) [115]. In addition, Next Generation Sequencing (NSG) showed the ability for the identification of genetic features of bacteria for detection of viral ability. The purpose of the clinical trial was the evaluation of NSG (Table 3) in the viral factor for detection of S. aureus in comparison to virulence factors that were identified by CCBA. NSG and CCBA were compared by the researchers in order to attain quick responses for the detection of factors causing virulence. NSG method was useful for description of diagnosis of bacterial strains in the diseased valve tissue and blood samples [116]. The information was gathered on the basis of evaluation of NSG-based prevalence in infective endocarditis. Furthermore, the NSG-guided antibiotic treatment was compared with standard of care therapy and the results were awaited [117].
Molecular sequencing technologies in the diagnosis and management of prosthetic joint infections
Published in Expert Review of Molecular Diagnostics, 2022
Zakareya Gamie, Dileep Karthikappallil, Emane Gamie, Stavros Stamiris, Eustathios Kenanidis, Eleftherios Tsiridis
There are various platforms for the analysis of the sequence data (fastq file generated by the sequencer) [55] for example, basic local alignment search tool (BLAST), burrow-wheeler aligner (BWA), and Cosmos ID. The processing time of BLAST can take several days and BLAST finds short matches between sequences and, therefore, is not ideal for metagenomics, especially using short reads; some metagenomic pipelines incorporate BWA, but the platform Cosmos ID does not use this aligner for their metagenomic classifications and directly gives an abundance score of the bacteria in the sample. Cosmos ID (https://www.cosmosid.com/platform) investigated recently [87], utilizes shotgun metagenomics and provides antimicrobial resistance (AMR) database results that list the resistance genes found. Machine learning-based algorithms are used to reduce the number of false positives obtained and are improved with more of the datasets analyzed from a wide variety of samples. Cosmos ID enables you to create a login, and provides example cases. Such platforms can use k-mer (subsequences contained within the sequence) matches to identify unique and shared regions of microbial genomes along a phylogenetic tree. By using microbial reference databases that follow the phylogenetic hierarchy of the represented microorganisms, this can enable reliable microbial identification down to strain level.
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